bin/mc_cdd

   1 #!/usr/local/bin/perl
   2
   3 use FindBin qw($Bin);
   4 use lib "$Bin/../lib";
   5
   6 # Don't edit the line below, it must look exactly like this.
   7 # Everything above this line will be replaced #
   8
   9 use PsN;
  10 use model;
  11 use tool::mc;
  12 use strict;
  13 use debug;
  14 use Getopt::Long;
  15 use common_options;
  16
  17 my $cmd_line = $0 . " " . join( " ", @ARGV );
  18
  19 ## Configure the command line parsing
  20 Getopt::Long::config("auto_abbrev");
  21
  22 my %options;
  23 ## Declare the options
  24
  25 my %required_options = ( 'case_column:s' => 'column_name|column_number',
  26                          'samples:i' => '100',
  27                          'alternative_model:s' => 'alt.mod' );
  28 my %optional_options = ( "bins:i" => '',
  29                          "selection_method:s" => '\'random\'|\'consecutive\'' );
  30
  31 my $res = GetOptions( \%options,
  32                       @common_options::get_opt_strings,
  33                       keys(%required_options),
  34                       keys(%optional_options) );
  35 exit unless $res;
  36
  37 my %help_text;
  38
  39 $help_text{Pre_help_message} = <<'EOF';
  40   mc_cdd
  41
  42     Perl script for Monte-carlo Simulation of Case-Deletion Diagnostics of NONMEM runs.
  43
  44   Usage:
  45 EOF
  46
  47 $help_text{Description} = <<'EOF';
  48     Description:
  49
  50       The Case Deletion Diagnostics tool is run from the command line
  51       with a few mandatory arguments. MC_CDD is run as a diagnostic after
  52       a model is regarded finished or at least mature enough to run
  53       validation tool on. You need to specify the NONMEM modelfile
  54       with a model that have successful termination. You also have to
  55       specify the number or name of the datafile column on which to
  56       select for deletion. You do so with the case_column option.
  57 EOF
  58
  59 $help_text{Examples} = <<'EOF';
  60     Example:
  61
  62       mc_cdd -model=run89.mod -case_column=10
  63
  64       This will perform a Case Deletion Diagnostic on the model
  65       specified in run89.mod based on the factors in column ten. If,
  66       for example, column ten holds the ids of the seven centers
  67       included in the study, this command will create seven copies of
  68       the dataset, each with individuals included in one specific
  69       center deleted. Say that the centers are numbered 1 to 7. Then
  70       dataset 1 will have individuals from center 1 excluded, dataset
  71       2 individuals from center 2 and so on.
  72 EOF
  73
  74 $help_text{Options} = <<'EOF';
  75     Options:
  76
  77       The options are given here in their long form. Any option may be
  78       abbreviated to any nonconflicting prefix. The -threads option
  79       may be abbreviated to -t(or even -thr) but -debug may not be
  80       abbreviated to -d because it conflicts with -debug_packages and
  81       -debug_subroutines.
  82
  83       The following options are valid:
  84 EOF
  85
  86 $help_text{-h} = <<'EOF';
  87       -h | -?
  88
  89       With -h or -? mc_cdd will print a list of options and exit.
  90 EOF
  91
  92 $help_text{-help} = <<'EOF';
  93       -help
  94
  95       With -help mc_cdd will print this, longer, help message.
  96 EOF
  97
  98 $help_text{-bins} = <<'EOF';
  99       -bins=$number
 100
 101       Sets the number of databins, or mc_cdd datasets, to use. If the
 102       number of unique values, or factors, in the based_on column is
 103       higher than the number of bins then one or more factors will be
 104       deleted in each mc_cdd dataset. Specifying $number as higher than
 105       the number of factors will have no effect. The bin number is
 106       then set to the number of factors.
 107       Default value = Number of unique values in the based_on column.
 108 EOF
 109
 110 $help_text{-selection_method} = <<'EOF';
 111       -selection_method='random' or 'consecutive'
 112
 113       Specifies whether the factors selected for exclusion should be
 114       drawn randomly or consecutively from the datafile.
 115       Default value = 'consecutive'
 116 EOF
 117
 118 $help_text{-case_column} = <<'EOF';
 119        -case_column=column_name|column_number
 120 EOF
 121
 122 $help_text{Post_help_message} = <<'EOF';
 123       Also see 'execute -help' for a description of common options.
 124 EOF
 125
 126 common_options::online_help( 'mc_cdd', \%options, \%help_text, \%required_options, \%optional_options);
 127
 128 ## Check that we do have a model file
 129 if ( scalar(@ARGV) < 1 ) {
 130   print "A model file must be specified. Use 'mc_cdd -h' for help.\n";
 131   exit;
 132 }
 133
 134 if( scalar(@ARGV) > 1 ){
 135   print "MC_CDD can only handle one modelfile. Use 'mc_cdd -h' for help.\n";die;
 136   exit;
 137 }
 138
 139 unless ( defined $options{'case_column'} ){
 140   print "case_column must be given\n" ;
 141   exit;
 142 }
 143
 144 unless ( defined $options{'alternative_model'} ){
 145   print "alternative_model must be given\n" ;
 146   exit;
 147 }
 148
 149 unless ( defined $options{'samples'} ){
 150   print "samples must be given\n" ;
 151   exit;
 152 }
 153
 154 ui -> category( 'mc_cdd' );
 155 ui -> silent(1) if( $options{'silent'} );
 156
 157 debug -> level( $options{'debug'} );
 158 debug -> package( $options{'debug_package'} );
 159 debug -> subroutine( $options{'debug_subroutine'} );
 160 debug -> warn_with_trace( $options{'warn_with_trace'} );
 161
 162 my $eval_string = common_options::model_parameters(\%options);
 163
 164 my $model = model -> new ( eval( $eval_string ),
 165                            filename                    => $ARGV[0],
 166                            ignore_missing_output_files => 1 );
 167
 168 my $alternative_model = model ->
 169     new ( eval( $eval_string ),
 170           filename                    => $options{'alternative_model'},
 171           ignore_missing_output_files => 1 );
 172
 173 ## Create new Mc_Cdd object:
 174 my $mc_cdd = tool::mc ->
 175     new ( eval( $common_options::parameters ),
 176           models             => [ $model ],
 177           alternative_models => [ $alternative_model ],
 178           samples            => $options{'samples'},
 179           subtools           => ['cdd'],
 180           subtool_arguments  => {
 181             bins             => $options{'bins'},
 182             selection_method => $options{'selection_method'},
 183             case_columns     => $options{'case_column'} } );
 184
 185 open(CMD, ">", $mc_cdd -> directory . "/command.txt");
 186 print CMD $cmd_line, "\n";
 187 close(CMD);
 188
 189 $mc_cdd -> run;
 190 $mc_cdd -> print_results;
 191